J Integr Plant Biol ›› 2018, Vol. 60 ›› Issue (1): 2-15.DOI: 10.1111/jipb.12606

• Functional Omics and Systems Biology •     Next Articles

Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)

Longyu Huang1,2, Mei Yang1, Ling Li1,2, Hui Li1,2, Dong Yang1, Tao Shi1* and Pingfang Yang1,3,4*   

  1. 1Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
    2University of Chinese Academy of Sciences, Beijing 100049, China
    3Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
    4Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
  • Received:2017-08-16 Accepted:2017-09-28 Published:2017-10-20
  • About author:**Correspondences: Email: Tao Shi (shitao323@wbgcas.cn); Pingfang Yang (yangpf@wbgcas.cn, Dr. Yang is fully responsible for the distribution of all materials associated with this article)


Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome, seed and flower lotus), one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and an outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation. We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.

Temperate and tropical lotus display high levels of genetic differentiation corresponding to ecological adaptation. Those genes contained in the highly differentiated genomic regions include those involving circadian clock and energy metabolism. Some of these candidate genes could be useful for molecular breeding of lotus lineages with long florescence in temperate zone.
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